Biochemical Genetics最新文献

{"title":"Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.","authors":"Abhishek Kumar, Tikam Chand Dakal, Kayenat Parveen, Ravi Bhushan, Bhanupriya Dhabhai, Alisha Parveen, Pankaj Yadav, Ravi Tandon","doi":"10.1007/s10528-026-11434-x","DOIUrl":"https://doi.org/10.1007/s10528-026-11434-x","url":null,"abstract":"<p><p>Integrating high-throughput sequencing with phylogenetic analysis now spans everything from single genes to long-read pangenomes and metagenomes, yet practitioners still face fragmented, tool-centric guidance. This review revisits algorithms, tools, and workflows for sequence and phylogenetic analysis in the NGS-based omics era, with a focus on comparative performance and scenario-driven decision-making. We first organise classical approaches to tree reconstruction - distance methods, maximum parsimony, maximum likelihood, and Bayesian inference - around core criteria of consistency, efficiency, robustness, and computational cost. We then examine multiple sequence alignment strategies, contrasting progressive, consistency-based, and structure-aware algorithms (such as MAFFT variants and T-Coffee family tools) with segment-based and incremental approaches (for example DIALIGN, anchored domains, and local updates) and alignment-free representations based on k-mers, absent words, and related statistics. For inference, we compare heuristic engines optimised for ultra-large alignments (FastTree, VeryFastTree, online tree optimisation) with full ML frameworks (IQ-TREE, RAxML-NG) and Bayesian platforms for time-scaled phylogenies and phylodynamics (MrBayes, BEAST family). We explicitly discuss trade-offs in accuracy, memory, scalability, and uncertainty support, and show how GPU-enabled implementations change the feasible design space. Beyond these core components, we address current trends that strongly influence method choice: long-read assemblies and pangenomes; data quality issues, contamination, recombination, and horizontal gene transfer; phylogenetic placement and alignment-free screening in metagenomics; and real-time pathogen surveillance using Nextstrain-style workflows. A dedicated section covers workflow management and containerisation (Snakemake, Nextflow, Docker/Singularity) together with benchmarking datasets and FAIR reporting, positioning reproducible pipelines as a first-class requirement rather than an afterthought. To make the review directly actionable, we provide a methodological checklist, a decision framework figure mapping input data to recommended strategies, and a large comparative table summarising algorithmic principles, best use cases, strengths, limitations, scalability, uncertainty support, and reproducibility notes for widely used tools. Applications in infectious disease genomics, oncology, and microbiome research illustrate how these choices translate into biological and clinical insight in practice.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148576704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shilajit as a Natural Product from Sedimentary Rocks: Biological Origin and Antioxidant Properties.","authors":"Asiye Ulug, Kezban Yildiz Dalginli, Funda Ozdemir Degirmenci, Melek Ozturkler Dundar, Onur Atakisi","doi":"10.1007/s10528-026-11428-9","DOIUrl":"https://doi.org/10.1007/s10528-026-11428-9","url":null,"abstract":"<p><p>Shilajit, a natural product with a documented history of use in traditional medicine for millennia, poses considerable challenges in elucidating its biological origin and pharmacological properties. In this study, a multidisciplinary approach integrating DNA metabarcoding and biochemical profiling was employed to investigate processed shilajit samples from the Pamir-Alai Mountains. Environmental DNA analysis identified 50 plant taxa across taxonomic levels ranging from order to species, indicating substantial botanical contributions to shilajit's composition. Among the identified taxa, Apiaceae and Asteraceae were the most represented families, while Vincetoxicum rossicum, Populus alba, and Quercus suber were the dominant species detected through metabarcoding analysis. Complementary biochemical analyses demonstrated notable antioxidant capacity and the presence of diverse bioactive compounds. Furthermore, oxidative stress-related biomarkers (NO, MDA, and GSH) were evaluated in the brain tissue of healthy rats following shilajit administration. No statistically significant differences were observed between the control and shilajit treated groups, suggesting that shilajit maintains physiological oxidative balance in healthy brain tissue. These findings provide important baseline biochemical data and support future investigations of shilajit's biological effects in validated oxidative stress and neurological disease models.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148576685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CircGABRB2_006 Drives Malignant Progression and EMT in Papillary Thyroid Carcinoma via the miR-296-5p/FGFR1 Axis.","authors":"Chuan Wan, Yanjun Guo, Han Guo, Jingjing Zhu, Fangchao Liu, Yunyuan Zhang, Bingfei Cheng, Juanjuan Li, Ying Xin, Bingzi Dong, Weiwei Fu, Dongmei Meng, Fang Wang, Shufa Li","doi":"10.1007/s10528-026-11436-9","DOIUrl":"https://doi.org/10.1007/s10528-026-11436-9","url":null,"abstract":"<p><p>Circular RNAs (circRNAs) have emerged as important regulators of tumor progression; however, their roles in papillary thyroid carcinoma (PTC) remain incompletely understood. In this study, we investigated the expression, biological function, and molecular mechanism of circGABRB2_006 in PTC. CircGABRB2_006 was significantly upregulated in PTC tissues and cell lines and was associated with aggressive clinicopathological characteristics, including increased tumor number, larger tumor size, advanced TNM stage, and lymph node metastasis. Functional assays demonstrated that circGABRB2_006 promoted PTC cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), tumor growth, and pulmonary metastasis, whereas its silencing exerted the opposite effects. Mechanistically, circGABRB2_006 predominantly localized in the cytoplasm and acted as a molecular sponge for miR-296-5p, thereby relieving miR-296-5p-mediated repression of fibroblast growth factor receptor 1 (FGFR1). Rescue experiments further confirmed that the oncogenic effects of circGABRB2_006 were largely dependent on the miR-296-5p/FGFR1 axis. Collectively, these findings demonstrate that circGABRB2_006 drives malignant progression of PTC through the miR-296-5p/FGFR1 signaling axis, highlighting its potential as a biomarker and therapeutic target in PTC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148576741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The m6A Reader IGF2BP2 Suppresses Ferroptosis in Nasopharyngeal Carcinoma by Stabilizing NRF2 mRNA.","authors":"Xiaoyan Xu","doi":"10.1007/s10528-026-11430-1","DOIUrl":"https://doi.org/10.1007/s10528-026-11430-1","url":null,"abstract":"<p><p>Nuclear factor erythroid 2-related factor 2 (NRF2) is a central transcriptional regulator of the antioxidant response and a key inhibitor of ferroptosis, and its overexpression is frequently observed in various cancers. However, the mechanisms underlying its dysregulation in nasopharyngeal carcinoma (NPC) remain poorly understood. In this study, we combined bioinformatic analysis with functional experiments to investigate the post‑transcriptional regulation of NRF2 in NPC. Using weighted gene co-expression network analysis (WGCNA) based on the GSE68799 dataset and differential expression analysis of NPC transcriptomic data, we identified NRF2 as a candidate gene associated with NPC progression. Functional studies confirmed that NRF2 inhibits ferroptosis in NPC cells. Mechanistically, we demonstrated that the m6A reader protein insulin‑like growth factor 2 mRNA‑binding protein 2 (IGF2BP2) binds to and stabilizes NRF2 mRNA in an m6A‑dependent manner. Depletion of IGF2BP2 downregulated NRF2 expression and accelerated NRF2 mRNA decay. Notably, inhibition of methyltransferase activity by S-Adenosyl-L-homocysteine (SAH) reduced m6A modification on NRF2 mRNA and impaired its interaction with IGF2BP2. Furthermore, IGF2BP2 knockdown impaired the NRF2/HO-1/GPX4 axis, leading to a significant reduction in GPX4 enzymatic activity and promoted ferroptosis, effects that were rescued by the NRF2 activator dimethyl fumarate (DMF). Collectively, these results reveal that IGF2BP2 stabilizes NRF2 mRNA via m6A modification to suppress ferroptosis, thereby promoting NPC cell survival.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148576670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of Genetic and Epigenetic Factors on Periodontitis Susceptibility and Treatment Outcomes.","authors":"Maryam Jalili Sadrabad, Parham Mohammadian Semnani, Farid Ghadyani, Nika Moghadamnia, Sahar Maleki, Mohammad Amin Hemmati, Majid Eslami","doi":"10.1007/s10528-026-11435-w","DOIUrl":"https://doi.org/10.1007/s10528-026-11435-w","url":null,"abstract":"<p><p>Periodontitis (PD) is a complex inflammatory condition driven by the interplay of microbial, genetic, epigenetic, and environmental factors. While bacterial biofilms are regarded as the primary cause, growing evidence underscores the significant role of genetic predisposition in determining susceptibility to the disease, its progression, and treatment outcomes. This review explores the genetic polymorphisms of PD, focusing on genes related to inflammatory mediators, immune responses, antimicrobial peptides, matrix metalloproteinases, and vitamin D receptor pathways. Key epigenetic mechanisms including DNA methylation, histone modifications, non-coding RNAs, and emerging RNA methylation pathways are explored in their roles in modulating inflammation, tissue destruction, bone metabolism, and interactions between the host and microbes. Advances in transcriptomic technologies, particularly RNA sequencing, have enhanced our ability to identify molecular biomarkers and cell-specific gene expression profiles associated with disease severity and responses to treatment. The potential for leveraging genetic and epigenetic profiling presents an exciting avenue for personalized periodontal care, including the use of epigenetic therapies targeting pathways involved in inflammation and tissue regeneration. Nonetheless, the current body of evidence has limitations. These include significant variability across studies, inconsistent disease classification systems, small sample sizes, and a predominance of preclinical or exploratory research. Many biomarkers and therapeutic targets proposed to date require further validation before they can be routinely applied in clinical practice. While integrating genetic, epigenetic, transcriptomic, and clinical data holds promise for advancing precision periodontology, rigorous large-scale, and multicenter studies are essential to confirm clinical applicability, validate biomarkers, and facilitate their incorporation into evidence-based treatment protocols.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148534877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovering New Orthologous Groups with P-COGs.","authors":"Dmitrii Sergeevich Bug, Dariia Andreevna Kuzovenkova, Artem Valerievich Tishkov, Natalia Olegovna Porozova, Natalia Vitalievna Petukhova","doi":"10.1007/s10528-026-11431-0","DOIUrl":"https://doi.org/10.1007/s10528-026-11431-0","url":null,"abstract":"<p><p>Deciphering the evolutionary history of genes is foundational for biomedical research, enabling the identification of compensatory mutations in disease-associated genes and the selection of evolutionarily relevant model organisms. However, challenges of multi-isoform handling, the presence of incomplete genomes/proteomes initial datasets, and problems of evolutionary history representation are still present. To address these issues, we introduce a novel framework based on the Clusters of Orthologous Groups (COG) method, primarily designed for improving phylogenetic tree clustering in studying evolutionary history of eukaryotes, P-COGs (Pavlov's COGs). It encourages the use of a single sequence dataset for both constructing phylogenetic trees and inferring COGs. We demonstrate the tool's utility through an evolutionary study of the voltage-dependent chloride channel genes family (CLCN). Moreover, P-COGs allowed us to observe multiple clusters of orthologous genes in CLCN that were not identified by other COG-based tools. Additionally, we resolved the evolutionary history of hundreds of cancer-associated genes with P-COGs to support accurate evolution-based variant effect prediction. The resulting COG graphs are accessible via our interactive web application ( https://epicenter.1spbgmu.ru/shiny/pavlovscogs/ ). P-COGs is openly available at https://github.com/bugds/Pavlovs_COGs .</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148534865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitogenome and Phylogeny of the Hairy Puffer Pao baileyi (Sontirat 1985).","authors":"Wei Hu, Xiao-Die Chen, Xiao Ma, Cheng-He Sun","doi":"10.1007/s10528-026-11433-y","DOIUrl":"https://doi.org/10.1007/s10528-026-11433-y","url":null,"abstract":"<p><p>The mitogenomics of Pao baileyi (Sontirat 1985), a tropical pufferfish with ornamental and research value, remain unreported. To understand its molecular characteristics and enrich mitogenome data for Tetraodontidae fish, in this study, we focused on the mitogenome of wild P. baileyi. The complete mitogenome sequence was obtained through high-throughput sequencing, and systematic analysis of the structural characteristics of the genome, base composition, and codon usage bias was conducted. A phylogenetic tree was constructed using Monacanthidae species as outgroups to explore the position of P. baileyi within Tetraodontidae. Results showed that the P. baileyi mitogenome is a closed-loop double-stranded DNA molecule with gene composition and arrangement conforming to Tetraodontidae mitogenome characteristics. It contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 1 control region. The base composition has an AT bias, codon usage exhibits specific preferences, and all tRNA genes have a cloverleaf secondary structure. Phylogenetic analysis revealed that P. baileyi is closely related to other Pao species and forms a distinct evolutionary branch with other genera and species in Tetraodontidae, providing a basis for species classification. This is the first report of the complete mitogenome characteristics of P. baileyi, providing basic data for phylogenetic relationships, germplasm resource conservation, and ornamental breeding research on Tetraodontidae fish.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"β-Eudesmol Alleviates Inflammatory Injury in Septic Cardiomyopathy Through Enhancing GSK3B Activity to Inhibiting IL-17-Mediated Chemokine Expression.","authors":"Sihua Jiang, Zhuoqing Dai, Tingting Pang, Ruobing Li, Xiaosong Wang, Hangqi Zhu, Guolin Song","doi":"10.1007/s10528-026-11427-w","DOIUrl":"https://doi.org/10.1007/s10528-026-11427-w","url":null,"abstract":"<p><p>Septic cardiomyopathy (SCM) is heart failure caused by sepsis and often causes an excessive inflammatory response. As a natural sesquiterpene alcohol, the anti-inflammatory properties of β-Eudesmol have been confirmed in various inflammatory diseases, but its effect on SCM remains unclear. Therefore, this study aimed to investigate the effect of β-Eudesmol on SCM and elucidate its potential mechanisms. An SCM rat model was established by cecal ligation and puncture (CLP) for experimental investigation. The levels of cytokines as well as the indicators of cardiac function injury, BNP and cTnl, were detected by ELSA. Myocardial tissue injury was detected by HE staining and TUNEL staining. The expression of key genes and proteins was detected by RT-qPCR and western blotting. The results show that treatment with β-Eudesmol alleviated myocardial apoptosis and inflammatory injury in SCM rats. Specifically, it significantly reduced serum levels of BNP and cTnI, and decreased the levels of IL-6, IL-1β, TNF-α, and LPS, while also inhibiting inflammatory cell infiltration and apoptosis within the myocardial tissue. Furthermore, we found that β-Eudesmol treatment also reduced serum IL-17 levels in rats and inhibited the expression of IL-17A, CXCL1, CXCL2, and CCL20 mRNA and p-GSK3B/GSK3B. Mechanistic studies revealed that β-Eudesmol enhanced GSK3B activity by inhibiting GSK3B phosphorylation, thereby suppressing the expression of IL-17 and its mediated chemokines, and ultimately alleviating inflammatory injury to the SCM. Overall, β-Eudesmol alleviates SCM myocarditis inflammation by inhibiting IL-17-mediated chemokine expression through enhancing GSK3B activity.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148429601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a Novel Slow-Gray STX17 Lineage in Japanese Thoroughbreds via a Multi-tiered Copy Number Analysis Workflow.","authors":"Koki Kawate, Risako Furukawa, Mio Kikuchi, Taichiro Ishige, Kazuhiro Seki, Teruaki Tozaki, Hironaga Kakoi","doi":"10.1007/s10528-026-11425-y","DOIUrl":"https://doi.org/10.1007/s10528-026-11425-y","url":null,"abstract":"<p><p>Gray is a dominant coat color phenotype in horses caused by a ~ 4.6 kb tandem triplication within intron 6 of syntaxin 17 (STX17). The copy number variation (CNV) of the duplicated segment influences the graying rate. The rare G2 allele (CNV = 2) is associated with a slower graying rate compared to the common G3 allele (CNV = 3) and is also relevant to melanoma risk. Current assays are limited because long and accurate PCR (LA-PCR) detects only the presence or absence of duplications, while droplet digital PCR (ddPCR) cannot reliably distinguish certain genotypes such as G3/g and G2/G2. We constructed a stepwise workflow combining (i) multiplex real-time PCR targeting the duplication junction for rapid gray/non-gray screening, (ii) ddPCR for copy number estimation, and (iii) LA-PCR for confirmatory genotyping of ambiguous copy-number classes. Using real-time PCR, we screened 4596 Japanese Thoroughbreds aged 2-7 years, of which 4374 were classified as non-gray and 222 as gray. Based on age and coat appearance, 23 Gy candidates were prioritized for slow-gray evaluation and analyzed by ddPCR; one was classified as G2/g, and 22 as G3/g or G2/G2. LA-PCR detected a g-derived band in all 22 cases, confirming that they were G3/g. Pedigree analysis suggested that the G2 allele was transmitted through the maternal line and that this lineage was distinct from the previously reported Japanese slow-gray family. This workflow enables practical molecular discrimination among non-gray, common gray, and slow-gray genotypes, supporting the surveillance of rare G2 alleles in the Japanese Thoroughbred population.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148417620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sexually Dimorphic RNA Helicase DDX3Y, But Not DDX3X, Plays a Potential Tumor-Suppressive Role in Colorectal Carcinogenesis in Males.","authors":"Suresh Govatati, Sravanthi Malempati, Roy Karnati, Gulam Hussain Syed, Sudip Ghosh, Raghava Rao Tamanam, Manjula Bhanoori, Pasupuleti Sreenivasa Rao","doi":"10.1007/s10528-026-11429-8","DOIUrl":"https://doi.org/10.1007/s10528-026-11429-8","url":null,"abstract":"<p><p>Beyond its role in sex determination, the Y chromosome contains genes that regulate transcription, translation, and protein stability, thereby contributing to the pathogenesis of various male-specific diseases, including cancer. Although sex significantly influences cancer incidence and outcomes, the molecular mechanisms underlying these differences remain poorly understood. These disparities are particularly evident in colorectal cancer (CRC), where men experience higher incidence, metastasis, and mortality rates. Here, we provide the first evidence that the sexually dimorphic RNA helicase DDX3Y (DEAD-box helicase 3 Y-linked), but not its X-linked homolog DDX3X, is significantly downregulated in tumor tissues from male CRC patients (n = 22). Overexpression of DDX3Y suppressed CRC cell proliferation, invasion, and colony formation while promoting apoptosis (p < 0.01). Conversely, siRNA-mediated depletion of DDX3Y, but not DDX3X, enhanced proliferation, invasion, and colony formation in normal colorectal mucosal cells (p < 0.01). Mechanistically, DDX3Y regulated the expression of key genes involved in cell growth and invasion, including KRAS, PIK3CA, PTEN, Snail, TCF7L1, and E-cadherin, whereas DDX3X had no significant effect on these targets. Collectively, these findings identify DDX3Y as a potential male-specific tumor suppressor in CRC and support further investigation of its prognostic and therapeutic potential in colorectal cancer.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148417729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}